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Bio::Tools::Signalp.3pm

NAME

Bio::Tools::Signalp - parser for Signalp output

SYNOPSIS

  use Bio::Tools::Signalp;
 
  my $parser = Bio::Tools::Signalp->new(-fh =>$filehandle );
 
  while( my $sp_feat = $parser->next_result ) {
    if ($sp_feat->score > 0.9) {
       push @likely_sigpep, $sp_feat;
    }
  }
 
 

DESCRIPTION

"SignalP" predicts the presence and location of signal peptide cleavage sites in amino acid sequences.

Bio::Tools::Signalp parses the output of "SignalP" to provide a Bio::SeqFeature::Generic object describing the signal peptide found, if any. It returns a variety of tags extracted from the NN and HMM analysis. Most importantly, the "score()" attribute contains the NN probability of this being a true signal peptide.

FEEDBACK

Mailing Lists

  User feedback is an integral part of the evolution of this and other
  Bioperl modules. Send your comments and suggestions preferably to
  the Bioperl mailing list.  Your participation is much appreciated.
 
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted va the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR

# Please direct questions and support issues to bioperl-l@bioperl.org

Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp originally written by Marc Sohrmann (ms2_AT_sanger.ac.uk). Written in BioPipe by Balamurugan Kumarasamy savikalpa_AT_fugu-sg.org. Cared for by the Fugu Informatics team (fuguteam_AT_fugu-sg.org)

CONTRIBUTORS

Torsten Seemann - torsten.seemann AT infotech.monash.edu.au

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

  Title   : new
  Usage   : my $obj = Bio::Tools::Signalp->new();
  Function: Builds a new Bio::Tools::Signalp object
  Returns : Bio::Tools::Signalp
  Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO
 
 

next_result

  Title   : next_result
  Usage   : my $feat = $signalp->next_result
  Function: Get the next result set from parser data
  Returns : Bio::SeqFeature::Generic
  Args    : none
 
 

_parse_hmm_result

  Title   : _parse_hmm_result
  Usage   : $self->_parse_hmm_result(\%feature)
  Function: Internal (not to be used directly)
  Returns : hash of feature values
  Args    : hash of more feature values
 
 

_create_feature

  Title   : _create_feature
  Usage   : $self->create_feature(\%feature)
  Function: Internal (not to be used directly)
  Returns : hash of feature values
  Args    : hash of more feature values
 
 

_seqname

  Title   : _seqname
  Usage   : $self->_seqname($name)
  Function: Internal (not to be used directly)
  Returns :
  Args    :
 
 

_fact1

  Title   : _fact1
  Usage   : $self->fact1($fact1)
  Function: Internal (not to be used directly)
  Returns : 
  Args    :